On Jelly Bean, using FX with root, I noticed duplicate files in /data/app-asec/, e.g.:
It looks like one is obsolete and consuming almost 60MB.
So I deleted the older ones of the duplicates and also renamed all files to have the suffix
After a reboot, some apps were not working. The launcher showed a "app is not installed" message.
After some more research, I found the file
/data/system/packages.xml which contains lines like these: